Bimetallic CoNi nanoparticles have been prepared within the apoferritin cavity. The protein shell controls size, prevents aggregation, and makes nanoparticles water-soluble. The CoNi series prepared in this way were structurally and magnetically characterized, the resulting magnetic properties varying accordingly with composition (Co(75)/Ni(25), Co(50)/Ni(50), Co(25)/Ni(75)). Co and Ni metals were associated in each nanoparticle, as demonstrated by high-angle annular dark field scanning electron microscopy and electron energy loss spectroscopy (EELS). After intentional oxidation, the CoNi nanoparticles were characterized by EELS, X-ray absorption near edge structure (XANES), and SQUID measurements to evaluate the importance of the oxidation on magnetic properties.